MmuINT0033996 @ mm9
Intron Retention
Gene
ENSMUSG00000029646 | Cdx2
Description
caudal type homeobox 2 [Source:MGI Symbol;Acc:MGI:88361]
Coordinates
chr5:148112476-148114902:-
Coord C1 exon
chr5:148114757-148114902
Coord A exon
chr5:148113670-148114756
Coord C2 exon
chr5:148112476-148113669
Length
1087 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TTCTATTTTGTCATCTCTAGGTT
3' ss Score
11.88
Exon sequences
Seq C1 exon
TGAAAACCAGGACAAAAGACAAATACCGGGTGGTGTACACAGACCATCAGCGGCTGGAGCTGGAGAAGGAGTTTCACTTTAGTCGATACATCACCATCAGGAGGAAAAGTGAGCTGGCTGCCACACTTGGGCTCTCCGAGAGGCAG
Seq A exon
GTGGGAATCGGCTTTCCTGGGTCTGGTTATTATGGCCTGGGGCAATCTTAATGGGTAGCATTAGAAAGTTTGGTCGAGGGAGCTGTTGCCTTTTGAGAATCCTTGAGTGTCCAGTTGTTTTTGCCGCTCTTTCAATGGATCAGAGAGCTGTAAGGGAAAAGCCAAGTCGAGGCTACAGGGTGGAACTGCACTTGGACAGAGAAAGAGCGATTGGAACCATGGTTCTCAACCTGTGGGTCGCGACCCCTCAGCTTGCCACTCAAACACGCTGTGCTTTATAATAGCAGCAAAATTATAGTTATGAAATAGCAATTAAAATAATTTGTGATTGGGGGTGTCACCACAACATGAAGAACTGTCCTAAAAAGAAAAACAAAGGTCCAGTCTACGCATACAAACTAAAGTCTGCTCATACAAATTAAAGAGGCAGGGGCTGGAGAGGTGATGCTTAAGAACACACACTCTTGCAGAGGATCGGAGTTCTGTTTCCAGCATCCACGTCAGGTGGCTCACAGTGTCACAGTGTCGGCTAACTCTGATTGCAGGGGACACCCAGTGCCTCTGGCTTCTGTGGATATATATGAATGTATACAGACATACACATATCAAAGATTTAAAAATCCTTGAACTTTTTTTTTCATTAACACAAAAGAGGCCCTACTTGCACACCAACACTTTCTGTAGTCTAGGGAAAAGGGAAGGAACAAACAAGAGAAATTCATAGCCAGGAAGTTTTGGACAAAGTTTCATTGTCTGTGCCAAGGTGAAGAACATCGCAGTACCAATGAGCTGTGGGAGCCCAAGGGTGACCCACGAGGCACACTGAGCTGGCCAACCATTTGTGTAGGGAATAGCTTTCGTCATGGTTCCGTTCCCTGGTTCTGAGGTTCTGTTGCTAGTAAAGGGTTTTTTGTTTGTTTGTTTTTTGTTTTTTGAAAGCAACTTGGGGAGGGGGCAGGTAAGTAAAGAGGACGAGGCTGGCCTGGCTTTGGGAACATTTCCCAAACTCAGTGAAAGAAGGACGCTCCCGGGGTGGCGCCATTTCTCTGTTCTTATCTTCTTCTACCTTCTATTTTGTCATCTCTAG
Seq C2 exon
GTTAAAATTTGGTTTCAGAACCGCAGAGCCAAGGAGAGGAAAATCAAGAAGAAGCAGCAGCAGCAACAGCAGCAGCAGCAACAACAGCCTCCACAGCCGCCGCCACAACCTTCCCAGCCTCAGCCGGGTGCCCTGCGGAGCGTGCCCGAGCCCTTGAGTCCTGTGACCTCCTTGCAAGGCTCAGTGCCTGGTTCTGTCCCTGGGGTTCTGGGGCCAGCTGGAGGGGTTTTAAACTCCACTGTCACCCAGTGACCCCTCCCGTGGTCTGAAGCGGCGGCGGCACAGCAATCCCAGGCTGAGCCATGAGGAGTATGGACGCTGCGAGAATCCTCAGAAGAGATTCCTCTCCTCCTACCCACGAACAGCATCTACTGATGGAGATTGAGGACAGAAGATGAGTGGAATTATGGACCTCAGGGGAAGACATGGTTTAGATTTTTTTTTTCTTTTTAACTTTTCCCATTCCGACTCTTCCTGCCAGCAACGACAAACGAAGTGATTCCTGGGGCTTCTTCGTTCATGCTCTTTGCCAGGACTGACTACCGACATGAAGCTATCAGCCTCTTTTGCCCCAGCTCTTTGCCTCTCTGTATTTCTGTGTGGAGCTGAGGAGAGAGTGAGACTGGATGGGGTGGGGGTAGCAATACTTGAGCCAAGGTGGCTGTTTCCTGCTGACTGCTTTCTGAGAACCAGCTGGCCGTCCTGCCTCCGGGCCAGGGACTATTCAAACTACAGGAGCCAGAGGCAGCTAAGATAGCTGGACTGACCGAAGTCTGCAGAACCTCCCCCACCAGGTGGTCTGGGCTTTCTTCTCCACAAATCAGGAAGGGGTGGTGGGTTCAGGGGCTGCGGTGAGAGGGGGTTGGTTAGCCAACGCCAGGCCCCTGCGACAAGGGCTTGTTTAGAAAGCCTGTCACCAGAGCTGCTGTAGGCGGAATGTATGTCTGTGTTGTAAATGCCAGAGCCAACCTGGACTTCCTGTCCCTTCCCTCGTCTTTGGCTGAAGAAGACCGGAATTGTTTGCTGCTGTTCGAGTCACTGATCTGTGTAACGAGCCAAACAAGCCTTTTAAAAAGCCTTCTTGATCCATGGGTAGAGAAGTTGTATGGTGAAGGGAAGTCGGGAGGGGGGGAAGGGGATCCGAACACAGTTGACTTTTATTTTGTAAAAAGACAAAGATAAACGAACTTTAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029646-Cdx2:NM_007673:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.306 A=NA C2=0.904
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=15.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTACACAGACCATCAGCGG
R:
TTTAAAACCCCTCCAGCTGGC
Band lengths:
347-1434
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: